Glycoside Hydrolase Family 137 - Revision history

Harry Brumer: Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

2021-12-18T21:17:49Z

Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

Alan Cartmell at 08:25, 12 May 2020

2020-05-12T08:25:04Z

Alan Cartmell at 08:23, 12 May 2020

2020-05-12T08:23:44Z

Alan Cartmell at 08:02, 12 May 2020

2020-05-12T08:02:56Z

Alan Cartmell at 20:32, 11 May 2020

2020-05-11T20:32:43Z

Alan Cartmell at 20:32, 11 May 2020

2020-05-11T20:32:02Z

Alan Cartmell at 19:26, 11 May 2020

2020-05-11T19:26:33Z

Harry Brumer at 19:24, 27 January 2020

2020-01-27T19:24:45Z

Harry Brumer: fixed missing biblio tag

2020-01-27T19:18:58Z

fixed missing biblio tag

Alan Cartmell at 16:02, 25 January 2020

2020-01-25T16:02:06Z

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
-* [[Author]]: ^^^Alan Cartmell^^^
+* [[Author]]: [[User:Alan Cartmell|Alan Cartmell]]
-* [[Responsible Curator]]:  ^^^Alan Cartmell^^^
+* [[Responsible Curator]]:  [[User:Alan Cartmell|Alan Cartmell]]
 ----

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 == Three-dimensional structures ==
-The structure of BT0996 comprises a single domain which is a five bladed β-propeller fold. Each blade is composed of three to four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. It should be noted that BT0996 is appended to a GH2 from clan GHA. This GH2 targets β-D-GlcA linkage in Chain A of RGII <cite>Ndeh2017</cite>.
+The structure of BT0996 comprises a single domain which is a five bladed β-propeller fold. Each blade is composed of three to four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. It should be noted that BT0996 is appended to a GH2 from clan GH-A. This GH2 targets β-D-GlcA linkage in Chain A of RGII <cite>Ndeh2017</cite>.
 == Family Firsts ==

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
-{{UnderConstruction}}
+{{CuratorApproved}}
 * [[Author]]: ^^^Alan Cartmell^^^
-* [[Responsible Curator]]:  ^^^Harry Gilbert^^^
+* [[Responsible Curator]]:  ^^^Alan Cartmell^^^
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 == Kinetics and Mechanism ==
-BT0996 was active both on intact RGII and on Chain B released from RGII <cite>Ndeh2017</cite>. A thorough mutagenic strategy was performed on BT0996 and identified two glutamates to be essential for activity, Glu159 and Glu240 (see below) <cite>Ndeh2017</cite>. The mechanism for arabinofuranosidedases are challenging to elucidate due to rapid tautomerisation of free arbinofuranose in solution to α and β anomers of both arabinopyranose (major confomer) and arabinofuranose.
+BT0996 was active both on intact RGII and on Chain B released from RGII <cite>Ndeh2017</cite>. A thorough mutagenic strategy was performed on BT0996 and identified two glutamates to be essential for activity, Glu159 and Glu240 (see below) <cite>Ndeh2017</cite>.  The mechanism for arabinofuranosidedases are challenging to elucidate due to rapid tautomerisation of free arbinofuranose in solution to α and β anomers of both arabinopyranose (major confomer) and arabinofuranose.
 == Catalytic Residues ==
-The catalytic residues were shown to be a pair of glutamates. They sit around 6 Angstroms apart. Typically retaining enzymes are expected to have their catalytic residues ~5.5 Angstroms apart, whilst in inverting enzymes they are expected to be ~10 Angstroms apart <cite>Davies1995</cite>.  Glu159 sits beneath the alpha face of the -1 β-linked arabinose, 3.2 Angstroms from the anomeric carbon, placing it in a an ideal position to act as a catalytic nucleophile. Glu240 resides 5 Angstroms from the glycosidic oxygen which somewhat far to act as catalytic acid/base in a retaining mechanism. Alternatively, one could also speculate that at a distance of 4.6 Angstroms from the anomeric carbon Glu240 could potentially act as a catalytic base in an inverting mechanism, with Glu159 acting as the catalytic acid being at a distance of 3.7 Angstroms from the glycosidic oxygen <cite>Ndeh2017</cite>.
+The catalytic residues were shown to be a pair of glutamates. The catalytic residue assignment was made based on both structural, substrate and product complexes, and mutagenic information. Glu159 and Glu240 were mutated to Ala and Gln. E159Q and E240A and E240Q were completely inactive, whilst E159A was only 26 fold less active. Despite the activity of E159A, these were the only residues that ablated activity.  They sit around 6 Angstroms apart. Typically retaining enzymes are expected to have their catalytic residues ~5.5 Angstroms apart, whilst in inverting enzymes they are expected to be ~10 Angstroms apart <cite>Davies1995</cite>.  Glu159 sits beneath the alpha face of the -1 β-linked arabinose, 3.2 Angstroms from the anomeric carbon, placing it in a an ideal position to act as a catalytic nucleophile. Glu240 resides 5 Angstroms from the glycosidic oxygen which somewhat far to act as catalytic acid/base in a retaining mechanism. Alternatively, one could also speculate that at a distance of 4.6 Angstroms from the anomeric carbon Glu240 could potentially act as a catalytic base in an inverting mechanism, with Glu159 acting as the catalytic acid being at a distance of 3.7 Angstroms from the glycosidic oxygen <cite>Ndeh2017</cite>.
 == Three-dimensional structures ==

@@ Line 32: / Line 32: @@
 == Kinetics and Mechanism ==
-BT0996 was active both on intact RGII and on Chain B released from RGII. A thorough mutagenic strategy was performed on BT0996 and identified two glutamates to be essential for activity, Glu159 and Glu240 (see below). The mechanism for arabinofuranosidedases are challenging to elucidate due to rapid tautomerisation of free arbinofuranose in solution to α and β anomers of both arabinopyranose (major confomer) and arabinofuranose.
+BT0996 was active both on intact RGII and on Chain B released from RGII <cite>Ndeh2017</cite>. A thorough mutagenic strategy was performed on BT0996 and identified two glutamates to be essential for activity, Glu159 and Glu240 (see below) <cite>Ndeh2017</cite>. The mechanism for arabinofuranosidedases are challenging to elucidate due to rapid tautomerisation of free arbinofuranose in solution to α and β anomers of both arabinopyranose (major confomer) and arabinofuranose.
 == Catalytic Residues ==

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 |-
 |'''Clan'''
-|GH-x
+|None
 |-
 |'''Mechanism'''
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 == Catalytic Residues ==
-The catalytic residues were shown to be a pair of glutamates. They sit around 6 Angstroms apart. Typically retaining enzymes are expected to have their catalytic residues ~5.5 Angstroms apart, whilst in inverting enzymes they are expected to be ~10 Angstroms apart.  Glu159 sits beneath the alpha face of the -1 β-linked arabinose, 3.2 Angstroms from the anomeric carbon, placing it in a an ideal position to act as a catalytic nucleophile. Glu240 resides 5 Angstroms from the glycosidic oxygen which somewhat far to act as catalytic acid/base in a retaining mechanism. Alternatively, one could also speculate that at a distance of 4.6 Angstroms from the anomeric carbon Glu240 could potentially act as a catalytic base in an inverting mechanism, with Glu159 acting as the catalytic acid being at a distance of 3.7 Angstroms from the glycosidic oxygen <cite>Ndeh2017</cite>.
+The catalytic residues were shown to be a pair of glutamates. They sit around 6 Angstroms apart. Typically retaining enzymes are expected to have their catalytic residues ~5.5 Angstroms apart, whilst in inverting enzymes they are expected to be ~10 Angstroms apart <cite>Davies1995</cite>.  Glu159 sits beneath the alpha face of the -1 β-linked arabinose, 3.2 Angstroms from the anomeric carbon, placing it in a an ideal position to act as a catalytic nucleophile. Glu240 resides 5 Angstroms from the glycosidic oxygen which somewhat far to act as catalytic acid/base in a retaining mechanism. Alternatively, one could also speculate that at a distance of 4.6 Angstroms from the anomeric carbon Glu240 could potentially act as a catalytic base in an inverting mechanism, with Glu159 acting as the catalytic acid being at a distance of 3.7 Angstroms from the glycosidic oxygen <cite>Ndeh2017</cite>.
 == Three-dimensional structures ==
@@ Line 49: / Line 49: @@
 <biblio>
 #Ndeh2017 pmid=28329766
-#Cantarel2009 pmid=18838391
+#Davies1995 pmid=8535779
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH137]]

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 == Substrate specificities ==
-The only activity identified to date is β-L-arabinofuranosidase activity displayed by the enzyme BT0996. This enzyme removes β linked L-arabinose from the terminus of side chain B in the complex glycan rhamnogalacturonan ii (RGII)<cite>Ndeh2017</cite>.
+The only activity identified to date is β-L-arabinofuranosidase activity displayed by the enzyme BT0996. This enzyme removes β linked L-arabinose from the terminus of side chain B in the complex glycan rhamnogalacturonan ii (RGII) <cite>Ndeh2017</cite>.
 == Kinetics and Mechanism ==
@@ Line 36: / Line 35: @@
 == Catalytic Residues ==
-The catalytic residues were shown to be a pair of glutamates. They sit around 6 Angstroms apart. Typically retaining enzymes are expected to have their catalytic residues ~5.5 Angstroms apart, whilst in inverting enzymes they are expected to be ~10 Angstroms apart.  Glu159 sits beneath the alpha face of the -1 β-linked arabinose, 3.2 Angstroms from the anomeric carbon, placing it in a an ideal position to act as a catalytic nucleophile. Glu240 resides 5 Angstroms from the glycosidic oxygen which somewhat far to act as catalytic acid/base in a retaining mechanism. Alternatively, one could also speculate that at a distance of 4.6 Angstroms from the anomeric carbon Glu240 could potentially act as a catalytic base in an inverting mechanism, with Glu159 acting as the catalytic acid being at a distance of 3.7 Angstroms from the glycosidic oxygen<cite>Ndeh2017</cite>.
+The catalytic residues were shown to be a pair of glutamates. They sit around 6 Angstroms apart. Typically retaining enzymes are expected to have their catalytic residues ~5.5 Angstroms apart, whilst in inverting enzymes they are expected to be ~10 Angstroms apart.  Glu159 sits beneath the alpha face of the -1 β-linked arabinose, 3.2 Angstroms from the anomeric carbon, placing it in a an ideal position to act as a catalytic nucleophile. Glu240 resides 5 Angstroms from the glycosidic oxygen which somewhat far to act as catalytic acid/base in a retaining mechanism. Alternatively, one could also speculate that at a distance of 4.6 Angstroms from the anomeric carbon Glu240 could potentially act as a catalytic base in an inverting mechanism, with Glu159 acting as the catalytic acid being at a distance of 3.7 Angstroms from the glycosidic oxygen <cite>Ndeh2017</cite>.
 == Three-dimensional structures ==
-The structure of BT0996 comprises a single domain which is a five bladed β-propeller fold. Each blade is composed of three to four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. It should be noted that BT0996 is appended to a GH2 from clan GHA. This GH2 targets β-D-GlcA linkage in Chain A of RGII<cite>Ndeh2017</cite>.
+The structure of BT0996 comprises a single domain which is a five bladed β-propeller fold. Each blade is composed of three to four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. It should be noted that BT0996 is appended to a GH2 from clan GHA. This GH2 targets β-D-GlcA linkage in Chain A of RGII <cite>Ndeh2017</cite>.
 == Family Firsts ==
 ;First stereochemistry determination: Not Known.
 ;First catalytic nucleophile/base identification: Inferred to be Glu159 in BT0996 <cite>Ndeh2017</cite>.
-;First general acid/base residue identification: Inferred to be Glu240 in BT0996<cite>Ndeh2017</cite>.
+;First general acid/base residue identification: Inferred to be Glu240 in BT0996 <cite>Ndeh2017</cite>.
-;First 3-D structure: The first structure determination for GH137 was of BT0996 from the organism ''Bacteroides thetaiotaomicon''<cite>Ndeh2017</cite>.
+;First 3-D structure: The first structure determination for GH137 was of BT0996 from the organism ''Bacteroides thetaiotaomicon'' <cite>Ndeh2017</cite>.
 == References ==

← Older revision		Revision as of 19:18, 27 January 2020
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	#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].		#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].

		+	</biblio>
	[[Category:Glycoside Hydrolase Families\|GH137]]		[[Category:Glycoside Hydrolase Families\|GH137]]